I have used chkdsk since windows 95 and it has, up until now, never deleted any of my files. Perhaps i never noticed, but if it had deleted any files, they were few at the most. But yesterday chkdsk reared its ugly face and upon me by fixing some sectors, and deleting over 40GB of my anniversay pictures that i had temporarily on my shared MAC/WINDOWS external drive...i was planning on transferring them that night. I didnt notice for the first hour since i didn't know chkdsk could do that. I dont usually run chkdsk but a sync program i use, called goodsync, forces me to have a clean drive. This wasnt new a procedure, i had done this many times before and never had any files gone missing.
I was lucky to find a program called unchk by eric p that finds and creates the files out of the .chk files that chkdsk created in a hidden "found.***" folder. It is a simple, free program. I still havent been able to recover all my files (still processing them) but i did retrieve about 30% of them since the files were orphaned. 80% of the my files were .cr2 format which didnt help since most .chk disk programs dont recognize this format. The good thing about unchk was that it allowed me to add the format type in the ini by opening the program, then on the first screen opening up the ini and adding or removing the extensions i needed and saving the file, then continuing.
In conclusion, never share an external drive on mac and windows. Windows will delete files that are fragmented, while mac won't.
Yesterday was a very sad moment for me as the loss was significant. It was a big trip with lots of memories and time spent taking over 40 gigs of photos.